Demo AUC

R/GCAT/man/GCAT.Rd

@@ -0,0 +1,20 @@
+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/GCAT.main.R
+\docType{package}
+\name{GCAT}
+\alias{GCAT}
+\alias{GCAT-package}
+\title{GCAT: Growth Curve Analysis Tool}
+\description{
+Mathematical modeling and parameter estimation of high volume microbial growth data.
+}
+\details{
+GCAT input is in .csv format.  GCAT analysis is accessed using \code{\link{gcat.analysis.main}}
+
+ GCAT utilizes the \code{\link[stats]{nls}} function in the R stats package to fit logistic, Gompertz and Richards models to growth curve
+ data. Best model is selected automatically.  Alternatively, the user may choose LOESS local regression fits, implemented using
+ \code{\link[stats]{loess}} function in the R stats package
+
+ Internally, the data are stored in an array of \linkS4class{well} objects
+}
+

R/GCAT/man/gcat.analysis.main.Rd

@@ -10,7 +10,7 @@ gcat.analysis.main(file.list, single.plate, layout.file = NULL,
   use.linear.param = F, use.loess = F, smooth.param = 0.1,
   lagRange = NA, totalRange = NA, totalODRange = NA, specRange = NA,
   points.to.remove = 0, remove.jumps = F, time.input = NA,
-  plate.nrow = 8, plate.ncol = 12, input.skip.lines = 0,
+  plate.nrow = 8, plate.ncol = 12, sranges = NA, input.skip.lines = 0,
   multi.column.headers = c("Plate.ID", "Well", "OD", "Time"),
   single.column.headers = c("", "A1"), layout.sheet.headers = c("Strain",
   "Media Definition"), silent = T, verbose = F, return.fit = F,
@@ -59,6 +59,8 @@ gcat.analysis.main(file.list, single.plate, layout.file = NULL,
 
 \item{plate.ncol}{The number of columns in a plate.}
 
+\item{sranges}{The 2 boundaries for calculating the area under the curve.}
+
 \item{input.skip.lines}{If specified, this number of lines shall be skipped from the top when reading the input file with read.csv}
 
 \item{multi.column.headers}{The headers of the result tabular data when analyzing multiple plates at once.}

R/GCAT/man/gcat.fit.main.Rd

@@ -10,7 +10,7 @@ gcat.fit.main(file.name, input.data = NULL, load.type = "csv",
   add.constant = 1, use.log = T, points.to.remove = 0,
   use.linear.param = F, use.loess = F, smooth.param = 0.1,
   fall.cutoff = -0.0025, growth.cutoff = 0.05, remove.jumps = F,
-  plate.nrow = 8, plate.ncol = 12, input.skip.lines = 0,
+  plate.nrow = 8, plate.ncol = 12, sranges = NA, input.skip.lines = 0,
   multi.column.headers = c("Plate.ID", "Well", "OD", "Time"),
   single.column.headers = c("", "A1"), layout.sheet.headers = c("Strain",
   "Media Definition"), growth.model = NA, backup.growth.model = NA,
@@ -63,6 +63,8 @@ By default(0) none are marked for removal.}
 
 \item{plate.ncol}{The number of columns in the input files.}
 
+\item{sranges}{The 2 boundaries for calculating the area under the curve.}
+
 \item{input.skip.lines}{If specified, this number of lines shall be skipped from the top when reading the input file with read.csv}
 
 \item{multi.column.headers}{The headers of the column when analyzing multiple plates.}

R/GCAT/man/gcat.output.main.Rd

@@ -8,9 +8,9 @@ gcat.output.main(fitted.well.array, out.prefix = "", source.file.list,
   upload.timestamp = NULL, add.constant, blank.value, start.index,
   growth.cutoff, points.to.remove, remove.jumps, out.dir = getwd(),
   graphic.dir = paste(out.dir, "/pics", sep = ""), overview.jpgs = T,
-  use.linear.param = F, use.loess = F, lagRange = NA, totalRange = NA,
-  totalODRange = NA, specRange = NA, plate.nrow = 8, plate.ncol = 12,
-  unlog = F, silent = T, main.envir)
+  sranges = NA, use.linear.param = F, use.loess = F, lagRange = NA,
+  totalRange = NA, totalODRange = NA, specRange = NA, plate.nrow = 8,
+  plate.ncol = 12, unlog = F, silent = T, main.envir)
 }
 \arguments{
 \item{fitted.well.array}{A list of fitted well objects.}
@@ -42,6 +42,8 @@ If NULL, defaults to the value of the first OD measurement of each well.}
 \item{overview.jpgs}{should jpgs be generated for each plate with the overview graphic?
 This is for backwards compatibility with the old web server.}
 
+\item{sranges}{The 2 boundaries for calculating the area under the curve.}
+
 \item{use.linear.param}{linear parameter is used or not?}
 
 \item{use.loess}{Is LOESS model going to be used?}

R/GCAT/man/plot-well-missing-method.Rd

@@ -8,7 +8,7 @@
 \S4method{plot}{well,missing}(x, y, constant.added = 1, xlim = NULL,
   ylim = NULL, well.number = NULL, scale = 1, number.points = T,
   draw.symbols = F, show.text = T, show.calc = T, draw.guess = NULL,
-  ...)
+  sranges = NA, ...)
 }
 \arguments{
 \item{x}{object of class well}
@@ -35,6 +35,8 @@
 
 \item{draw.guess}{initial guess model.  Drawn if specified}
 
+\item{sranges}{The boundaries to calculate the AUC.}
+
 \item{...}{additional arguments passed to the generic plot function}
 }
 \description{

R/GCAT/man/well-class.Rd

@@ -44,5 +44,7 @@ Class that contains well data
 \item{\code{loess}}{- object returned by running loess on the normalized well data}
 
 \item{\code{nls}}{- object returned by running nls on the normalized well data}
+
+\item{\code{auc}}{- The area under the curve.}
 }}